Commands¶

ReSeq2 provides five commands, each accessible as a sub-command of the reseq2 binary.

reseq2 <command> [options]

illuminaPE¶

Full paired-end simulation pipeline. This is the primary command and covers the entire workflow: collecting sequencing statistics from a BAM file, estimating multi-dimensional probability distributions via Iterative Proportional Fitting, and simulating realistic paired-end reads. Each stage can be run independently by combining the appropriate flags (--statsOnly, --stopAfterEstimation, --ipfIterations 0).

reseq2 illuminaPE -j 32 -r ref.fa -b reads.bam -1 sim_R1.fq -2 sim_R2.fq

seqToIllumina¶

Apply the Illumina error and quality model directly to input sequences. Use this when the coverage model is not applicable --- for example, when simulating reads from synthetic or designed sequences. It adds quality scores, substitution errors, and InDel errors, and trims sequences to the read length (appending adapter sequence if the input is shorter).

reseq2 seqToIllumina -j 2 -i sequences.fa -o reads.fq -s profile.reseq

See Error Model for the required input FASTA format and workflow details.

queryProfile¶

Extract summary information from a .reseq stats file. Useful for inspecting fragment-length bias, reference-sequence bias, maximum read length, or longest detected deletion without running a full simulation.

reseq2 queryProfile -s profile.reseq --fragLenBias bias.tsv

replaceN¶

Replace ambiguous bases (N and other IUPAC codes) in a reference FASTA with random A/C/G/T. Running this once before simulation ensures that the same replacement is used consistently across multiple simulation runs with the same reference.

reseq2 replaceN -r ref_with_ns.fa -R ref_clean.fa --seed 42

convertProfile¶

Convert stats and probability files between binary and text formats. Binary format is the default (smaller, faster) but is not portable across CPU architectures or compilers. Text format is portable and suitable for sharing or archiving.

# Binary to text
reseq2 convertProfile -s profile.reseq --textFormat

# Text to binary
reseq2 convertProfile -s profile.reseq

See Profiles for a detailed discussion of format trade-offs.

For the full list of options for each command, see Parameters.